I don't disagree with the idea of the tadpole giving more power to tempt us right from the start. However, again, if they do nothing to make releasing SH NOT a temptation to do something we may later regret, why NOT release her, every time? Suddenly introduce a mind flayer power temptation, and whoa. Wait a minute. Maybe I should rethink this.

As for why? She had it hidden on her, and they didn't have time to extract it before the Gith showed up and it was all hands on deck to ward off the attacks. Best just to seal her in a coffin for now and deal with the rebellious witch later. Make it so only a mind flayer can access it to ensure it is secure.

Again, just one possible explanation. Who knows what Larian's true reasoning is.